scholarly journals DiaThor: R package for computing diatom metrics and biotic indices

2021 ◽  
Author(s):  
Maria Mercedes Nicolosi Gelis ◽  
Maria Belen Sathicq ◽  
Jonathan Jupke ◽  
Joaquin Cochero
Keyword(s):  
Water Quality ◽  
Web Application ◽  
Water Quality Assessment ◽  
R Package ◽  
Morphological Data ◽  
Sensitivity Index ◽  
Biotic Indices ◽  
Ecological Data ◽  
Diatom Index ◽  
Open Platform

1- Diatoms are widely used to detect changes in water quality due to their specific sensibility to a variety of environmental conditions. Among the different diatom-based tools to measure water quality, the biotic indices, ecological and morphological traits are the most commonly used. 2- DiaThor, contains 19 functions that provide morphological data of the samples (number and shape of chloroplasts, total biovolume), ecological data (species richness, evenness, diversity, size classes, ecological guilds, ecological preferences) and biotic indices (Descy Index, EPID Index, Indice Diatomique Artois-Picardie, Swiss Diatom Index, Pampean Diatom Index, ILM index, Specific Pollution sensitivity Index, Lobo Index, Sladecek index, SPEAR(herbicides) index and the Trophic index). A web application (in Shiny) was also developed to provide access to the package for those users not familiar with the R environment. 3- The structure of the package, how it functions and the structure of the input and output data are explained. To demonstrate the most common use of DiaThor, an example of the package performance is also provided. 4- The DiaThor package aims to contribute to the water quality assessment based on diatom assemblages, while also providing researchers with an open platform to suggest new statistics and functionalities to be integrated into future builds.

scholarly journals Use of Diatoms in Monitoring the Sakarya River Basin, Turkey

Water ◽  
2020 ◽  
Vol 12 (3) ◽  
pp. 703 ◽  
Author(s):  
Cüneyt Nadir Solak ◽  
Łukasz Peszek ◽  
Elif Yilmaz ◽  
Halim Aytekin Ergül ◽  
Melih Kayal ◽  
...  
Keyword(s):  
Water Quality ◽  
River Basin ◽  
Water Quality Assessment ◽  
Sensitivity Index ◽  
Diatom Index ◽  
Diatom Indices ◽  
Sakarya River ◽  
Important Correlation ◽  
Water Quality Status ◽  
Quality Status

The Sakarya River basin is one of the largest basins in Turkey, and encompasses the Kocaeli, Düzce, Sakarya, Bursa, Bilecik, Bolu, Kütahya, Eskişehir, Ankara, Afyon, and Konya provinces. In this study, the water quality status of the basin was investigated using 18 diatom indices, calculated in Omnidia software. For this purpose, a total of 46 stations were surveyed in the rivers and streams of the basin in May 2018. As a result, 41 of 195 diatom taxa were found to be the most frequent (>10% share in assemblage). According to Detrented Correspondence Analysis (DCA), three subgroups were described as the spring section, Ankara and Polatlı section, and lowland section. The river basin quality was evaluated as moderate or lower quality status, while only a few sites had good status. The diatom index scores showed that the Descy’s Index (DES), Pampean Diatom Index (IDP), Artois-Picardie Diatom Index (IDAP), and Specific Pollution Sensitivity Index (IPS) appear best suited to water quality assessment in this area, showing the largest number of significantly important correlation with environmental variables.

Grey Correlation Model Based on Diatom Indices Evaluating Water Quality of Longjiang River

2013 ◽  
Vol 448-453 ◽  
pp. 43-47 ◽  
Author(s):  
Xin Tang ◽  
De Suo Cai ◽  
Wen Ting Yao
Keyword(s):  
Water Quality ◽  
Water Quality Assessment ◽  
Quality Standard ◽  
Relational Model ◽  
Water Quality Standard ◽  
Diatom Index ◽  
Model Based ◽  
Diatom Indices ◽  
Grey Relational

In order to evaluate the water quality of Longjiang river comprehensively, diatoms of 15 sampling sites are collected to establish the Grey Relational Model based on three diatom indexesIPS, IBD and IDG. From the Cluster analysis of sampling sites and the box plot of diatom index, IBD is the best, then the IPS, the diatom index weights on water quality assessment are 0.637 for IBD, 0.2583 for IPS, 0.1074 for IDG respectively. Finally, by comparing the water quality standard level based on Grey Relational Model, it can be known that the water quality of most sampling sites is fine except that site No.1 and No.3 belong to III water quality standard. The result shows that it is more comprehensive and reasonable to use the Grey Relational Model based on diatom index rather than individual diatom index to assess water quality.

scholarly journals The Application of Benthic Diatoms in Water Quality Assessment (Mlava River, Serbia)

2016 ◽  
Vol 75 (2) ◽  
pp. 199-205 ◽  
Author(s):  
Olga S. Jakovljević ◽  
Slađana S. Popović ◽  
Danijela P. Vidaković ◽  
Katarina Z. Stojanović ◽  
Jelena Ž. Krizmanić
Keyword(s):  
Water Quality ◽  
Ecological Status ◽  
Detrended Correspondence Analysis ◽  
Pollution Index ◽  
Water Hardness ◽  
Nutrient Concentrations ◽  
Sensitivity Index ◽  
Temperature Conductivity ◽  
Diatom Index ◽  
Diatom Indices

AbstractThe main objective of this study was to assess the ecological status of the Mlava River based on epilithic diatoms and to test the use of diatom indices as a tool for estimating the quality of flowing waters in Serbia. Quantitative analysis showed that in AprilAchnanthidium minutissimumwas dominant at each site, except at the fifth site, whereAmphora pediculuswas dominant. In July and September,Achnanthidium minutissimum, Achnanthidium pyrenaicum,Amphora pediculus,Denticula tenuis,Diatoma vulgaris,Gomphonema elegantissimum,Cocconeis pseudolineataandCocconeis placentulavar.lineatadominated. Detrended correspondence analysis (DCA) was used to detect the major patterns of variation in species composition. The first DCA axis summarizes the distribution of the diatom community, mainly through temperature, conductivity, oxygen and water hardness gradient. The second DCA axis was weakly correlated with few variables. Based on the average values of the pollution sensitivity index (IPS), commission for economical community metric (CEE) and biological diatom index (IBD), the water of the Mlava River belonged to water class I during all three seasons. Values of the diatom-based eutrophication/pollution index (EPI-D) indicated class II water quality. According to calculated trophic diatom index (TDI) values, water of the Mlava River was characterized by intermediate nutrient concentrations during three seasons. Principal components analysis was used to represent the correlation between diatom indices, and the highest correlation among the selected diatom indices is seen between EPI-D, IPS and IBD.

scholarly journals Diatom diversity and water quality of a suburban stream: a case study of the Rzeszów city in SE Poland

2016 ◽  
Vol 41 (1) ◽  
pp. 19-34 ◽  
Author(s):  
Teresa Noga ◽  
Jadwiga Stanek-Tarkowska ◽  
Urszula Kloc ◽  
Natalia Kochman-Kędziora ◽  
Mateusz Rybak ◽  
...  
Keyword(s):  
Water Quality ◽  
Ecological Status ◽  
Sensitivity Index ◽  
Diatom Assemblages ◽  
Diatom Index ◽  
Se Poland ◽  
Physicochemical Factors ◽  
Index Index ◽  
The City

Abstract The aim of this work was to investigate the diversity of diatom assemblages developed in the Przyrwa stream, to assess water quality based on benthic diatoms and to make an attempt at the identification of physicochemical factors having the greatest impact on the differentiation of diatom assemblages. Studies were conducted in 2011-2012 on the Przyrwa stream, a left-side tributary of the Wisłok River flowing through the city of Rzeszów and with its spring section located on the borders of the city. A total of 259 diatom taxa were identified in the Przyrwa stream during three studied seasons. At all investigated sites, the most abundant population consisted of Ulnaria ulna (Nitzsch) Compère, Cocconeis pediculus Ehrenb., Achnanthidium minutissimum (Kütz.) Czarnecki var. minutissimum, Navicula gregaria Donkin, Planothidium frequentissimum (Lange-Bert.) Lange-Bert., P. lanceolatum (Brébisson) Lange-Bert., Navicula lanceolata (C. Agardh) Ehrenb., Amphora pediculus (Kütz.) Grunow, Eolimna minima, (Grunow) Lange-Bert., Melosira varians C. Agardh and Cyclotella meneghiniana Kütz. Based on IPS (Specific Pollution Sensitivity Index) and GDI (Generic Diatom Index) indices, the ecological status of the Przyrwa stream was assessed as moderate to poor (mostly III-IV class of water quality), while the TDI (Trophic Diatom Index) index indicated a poor to bad ecological status (mainly IV-V class of water quality).

scholarly journals Research into the Epipelic Diatoms of the Meriç and Tunca Rivers and the Application of the Biological Diatom Index in Water Quality Assessment

2019 ◽  
Vol 35 (1) ◽  
pp. 19-26 ◽  
Author(s):  
Cem Tokatlı ◽  
Cüneyd Nadir Solak ◽  
Elif Yılmaz ◽  
Tahir Atıcı ◽  
Hayri Dayıoğlu
Keyword(s):  
Water Quality ◽  
Quality Assessment ◽  
Water Quality Assessment ◽  
Diatom Index ◽  
Epipelic Diatoms

scholarly journals Assessment of seasonal differences of ecological state of lotic ecosystems and applicability of some biotic indices in the basin of Lake Sevan (Armenia): case study of Masrik River

2018 ◽  
Vol 19 (4) ◽  
pp. 1238-1245 ◽  
Author(s):  
V. L. Asatryan ◽  
M. R. Dallakyan
Keyword(s):  
Water Quality ◽  
Water Quality Assessment ◽  
Biotic Indices ◽  
Ecological State ◽  
Reference Sites ◽  
Seasonal Differences ◽  
Qualitative And Quantitative ◽  
Different Parts ◽  
Bioindication Methods

Abstract Complex studies of seasonal differences of the ecological state of Masrik River (Armenia) were realized in 2017. Water quality was assessed by BMWP, ASPT and FBI indices based on studies of qualitative and quantitative structures of benthic macro-invertebrates. Potential reference sites in the basin were revealed using the %EPT taxa index in addition to water quality assessment by bioindication methods as well as hydro-chemical, -physical and -morphological measurements. The applicability of the used biotic indices for the different parts of Masrik River was discussed.

Demonstration of the Bzura River restoration using diatom indices

Biologia ◽  
2011 ◽  
Vol 66 (3) ◽  
Author(s):  
Barbara Rakowska ◽  
Ewelina Szczepocka
Keyword(s):  
Water Quality ◽  
Benthic Diatom ◽  
Biological Assessment ◽  
Sensitivity Index ◽  
Running Waters ◽  
Class Iii ◽  
Gradual Improvement ◽  
Diatom Index ◽  
Diatom Indices ◽  
The Impact

AbstractThe quality of running waters is reflected in the composition of benthic diatom assemblages. The biological assessment of changes in the composition, and thus of changes in water quality, was carried out in the lowland mid-sized Bzura River, Central Poland, over the period of 30 years. The benthic diatom material consisted of samples collected in two investigation periods, in 1972 and in 2003–2004. The methods applied were three diatom indices, IPS — Specific Pollution Sensitivity Index, GDI — Genetic Diatom Index and TDI —Trophic Diatom Index, and the OMNIDIA computer program, which are commonly used in Europe. The aim of the study was demonstrating the process of restoration that occurred in the river. The Bzura was included to the most polluted ones in Poland till 1996. Since 1998 a gradual improvement in water quality has been observed, which is caused by a number of biological-technical measures, mostly a proper organization of sewage management in most cites located on the river. In 1972 the IPS classified Bzura water into Water Quality Class IV-V, while in 2003–2004 it reached much higher values, i.e. Class III–IV. On the basis of the GDI Class III was determined in the whole river in 2003–2004, while its values indicated Class III–IV in 1972. The trophic index, TDI attributed Bzura water to the eutrophic to hypereutrophic zone in 2003–2004, and to one degree better water, i.e. from the mesoeutrophic to eutrophic zone, in 1972.From the carried out research it follows that the IPS is the best index, which may be commonly applied to assess saprobic pollution of running waters in Poland. It indicated an improvement in water that occurred in the Bzura over 30 years and took into account the impact of pollution sources and tributaries in given river sections.

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